Sydney Bristow is a spy. She works for SD-6, which she thinks is part of the CIA.  Sydney is also a graduate student in English lit, although she seems to spend more time studying C4 than Fitzgerald.

Sydney falls in love with a nice young doctor, he proposes, and she confesses to him that he will be marrying a part-time spy.  Her fiancé Danny leaves a message on her answering machine while she is away, saying the spy thing is OK by him. When Syd returns, she finds Danny killed.  (Hey, is he dead, or is he just on a different planet, or maybe in a different time period?)

Sydney goes to Arvin Sloane, the director of SD-6, who admits that fiancé was killed by SD-6, and that Syd knew the rules when she signed on - anyone who finds out about SD-6 is killed. Syd is not happy with Sloane or SD-6, and so she quits and walks out. Which is also against the rules, and which sends the SD-6 hit squad after her.

As she is trying to escape the hit men, Syd gets a lift from an unlikely source, namely her estranged dad Jack Bristow. She hasn't had a lot to do with Jack since her mother died when she was 7.  Jack surprises Syd with the announcement that instead of selling airplane parts like she thought, he is also a spy for SD-6. He also explains that SD-6 is not part of the CIA, but is part of the bad guys, the infamous Alliance of 12.

Syd has an idea that might save her life as well as bring down SD-6. She goes to Hong Kong to complete her previous mission for SD-6, stealing a funny-looking metal cradle and red ball thingy. After much daring-do, she marches into Sloane's office and announces she is back on the job. Then she marches out again.

Syd keeps marching all the way to the CIA, where she offers her services as a double agent to infiltrate SD-6 for them. This sounds good to CIA agent Michael Vaughn, who will be her contact/handler. (Hey, does he look familiar? Try in a different time period ) Vaughn reveals that she will be one of two double agents at SD-6. The other double agent is her father, Jack Bristow.

So begins Syd's life as a double agent. She wears lots of wigs Syd works with her nice SD-6 partner Dixon, who thinks he works for the CIA. She gets lots of gizmos for her missions from Marshall, SD-6's Q.

The usual double agent scenario: Syd gets a mission assigned by SD-6. Then she meets with Vaughn, usually in a self-storage building, and tells him all. He tells her what the CIA wants her to do on the mission - like making copies or substituting fake stuff for real. After the mission, she hands over the goods and info to Vaughn.

In Sydney's other life, she has two close friends, her housemate Francie and her reporter friend Will Tippin Francie is finishing MBA stuff and is planning to open a restaurant some day. She gets engaged to a schmuck, but that falls through. She has no idea what Syd does, and has no strong storyline in the season.

Reporter Will Tippin wants to help Syd. He just wants to find fiancé Danny's murderers, despite the pleas from Syd to let it go. He gets some mysterious aid from an anonymous caller who puts him on the track of a mysterious organization called SD-6.

Meanwhile, Sydney discovers Russian ciphers in some books that her dad had bought for her mother. She gives them to Vaughn for analysis. The deciphered messages contain orders that directly relate to the murders of 12 CIA agents twenty-odd years before. Including Vaughn's father. Syd and Vaughn think dad Jack was a KGB spy, but Jack and CIA officials explain that the spy was not Jack, but Syd's mom.

All spies everywhere are after everything Rambaldi. Rambaldi was a 15th century inventor and prognosticator. His inventions were often centuries ahead of their time. 47 is his special number. There are manuscripts, inventions, machines with encoded information. All of the prophesies Rambaldi made have been found to be true - much better track record than Nostradamus.

At the front of the Rambaldi hunt is an organization with no name, headed by "The Man", who is believed to be Khasinau, ex-KGB. Also identified with this organization is a hit man named Sark. One prophesy says that a great evil will be unleashed, caused by a woman. Syd fits the picture and all of the physical pointers. But so does Syd's mom, whom Syd and Jack learn did not die. Now the CIA and Syd are trying to find Mom, but for different reasons.

Will's research is discovered by SD-6. Jack tries to stop Will without killing him. Will is kidnapped by masked men, is threatened effectively, and ceases. He's now off of the SD-6 hit list. But then his informant tells him the masked man was Jack. Will goes to see Jack for answers, after leaving his story with a friend to be published in case he disappears. Jack says he's a good guy and asks for Will's help to find the identity of Will's informant.

Arvin Sloane's wife Emily is dying of cancer. Unfortunately, she reveals in a conversation with Syd that is being monitored by SD-6, that she knows about SD-6. The rules say that she must be killed, but Sloane pleads for her life with the Alliance. He says she is being killed already by her cancer. She is granted a reprieve, but then she goes into remission. Once again Sloane is told that she must die. So he takes her to a lovely seaside cottage and offers her a glass of doctored wine.

Will dangles a carrot to flush out the tipster. He mentions "the circumference", which Jack tells him to do. Tipster directs Will to meet him in Paris, and brings him at gunpoint to a nightclub owned by Khasinau.  Sydney, on assignment to track Khasinau and not informed by her dad about Will, sees this happening. Will gets a big surprise as he watches Syd go into spy mode and rescue him from the bad guys.

Will is put in a CIA safe house, where Syd visits him and explains that she really can't explain about her life. Unfortunately, Sark kidnaps Will and takes him to Taipei for interrogation and torture. They want to find out what he knows about "the circumference"  (nothing). And they want a ransom for his life, demanded from Syd. They want a missing Rambaldi page.

Syd and Jack decide to ransom Will themselves. They steal the Rambaldi page and arrange to take it to Taipei Vaughn suspects that they are going to do something like this. Even though he is under orders not to get too involved, he decides to privately offer his help. So Syd, Jack and Vaughn fly to Taipei.

Jack successfully trades the Rambaldi page for Will and gets a big hug from a grateful Will. Meanwhile, Syd and Vaughn go to a warehouse where Khasinau's people are building this circumference, which is a gigantic version of what Syd stole earlier in the season. They need to destroy it.

When they do, that big red ball thingy breaks open and floods the corridors with water. Syd barely escapes, but Vaughn is caught in the flood. Syd tries desperately to free him, but is caught herself by the bad guys. When she comes to, Syd discovers that she is a prisoner of 'The Man', and that this person is actually her mother, Laura Bristow, aka Irina Derevko.

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